(Module): Clarifications on computing e.j

diff --git a/src/imach.c b/src/imach.c
index f6cb878fa498efd95fa5cd8bc241c466907af506..9e7cfe106cbd0580ff3b065b061d0c3a8db1cc6f 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,18 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.127  2006/04/28 18:11:50  brouard
+  (Module): Yes the sum of survivors was wrong since
+  imach-114 because nhstepm was no more computed in the age
+  loop. Now we define nhstepma in the age loop.
+  (Module): In order to speed up (in case of numerous covariates) we
+  compute health expectancies (without variances) in a first step
+  and then all the health expectancies with variances or standard
+  deviation (needs data from the Hessian matrices) which slows the
+  computation.
+  In the future we should be able to stop the program is only health
+  expectancies and graph are needed without standard deviations.
+
   Revision 1.126  2006/04/28 17:23:28  brouard
   (Module): Yes the sum of survivors was wrong since
   imach-114 because nhstepm was no more computed in the age
@@ -374,7 +386,7 @@ extern int errno;
 /* $Id$ */
 /* $State$ */
 
-char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
+char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
 char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
@@ -1332,10 +1344,11 @@ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, in
     for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {
        po[i][j][h]=newm[i][j];
-       /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
-        */
+       /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }
+    /*printf("h=%d ",h);*/
   } /* end h */
+/*     printf("\n H=%d \n",h); */
   return po;
 }
 
@@ -2252,7 +2265,8 @@ void prevalence(double ***probs, double agemin, double agemax, int **s, double *
          if( i <=  iagemax){ 
            if(posprop>=1.e-5){ 
              probs[i][jk][j1]= prop[jk][i]/posprop;
-           } 
+           } else
+             printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
          } 
        }/* end jk */ 
       }/* end i */ 
@@ -2856,7 +2870,7 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double
   pstamp(ficresvij);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if(popbased==1)
-    fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+    fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   else
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fprintf(ficresvij,"# Age");
@@ -2884,8 +2898,7 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin. 
-     Look at hpijx to understand the reason of that which relies in memory size
-     and note for a fixed period like k years */
+     Look at function hpijx to understand why (it is linked to memory size questions) */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed every two years of age and if
@@ -2951,7 +2964,7 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double
        }
       }
 
-      for(j=1; j<= nlstate; j++){
+      for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
        for(h=0; h<=nhstepm; h++){
          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
@@ -3511,7 +3524,7 @@ void printinghtml(char fileres[], char title[], char datafile[], int firstpass,
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
           subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(fichtm,"\
- - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+ - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n",
           estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
    fprintf(fichtm,"\
@@ -3576,11 +3589,11 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    <a href=\"%s\">%s</a> <br>\n</li>",
           estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
  fprintf(fichtm,"\
- - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
         estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
  fprintf(fichtm,"\
- - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
-        subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+        estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
  fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
         subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
@@ -3613,7 +3626,10 @@ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png<br>\
+health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+true period expectancies (those weighted with period prevalences are also\
+ drawn in addition to the population based expectancies computed using\
+ observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */
  }/* End k1 */
@@ -4376,6 +4392,7 @@ int main(int argc, char *argv[])
   int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;
   int NDIM=2;
+  int vpopbased=0;
 
   char ca[32], cb[32], cc[32];
   char dummy[]="                         ";
@@ -5851,47 +5868,49 @@ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
  
        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
-       if(popbased==1){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-       }
-
        pstamp(ficrest);
-       fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-       fprintf(ficrest,"\n");
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         oldm=oldms;savm=savms;
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+         if(vpopbased==1)
+           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+         else
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         fprintf(ficrest,"# Age e.. (std) ");
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
 
-       epj=vector(1,nlstate+1);
-       for(age=bage; age <=fage ;age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         if (popbased==1) {
-           if(mobilav ==0){
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=probs[(int)age][i][k];
-           }else{ /* mobilav */ 
-             for(i=1; i<=nlstate;i++)
-               prlim[i][i]=mobaverage[(int)age][i][k];
+         epj=vector(1,nlstate+1);
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           if (vpopbased==1) {
+             if(mobilav ==0){
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */ 
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
+             }
            }
-         }
        
-         fprintf(ficrest," %4.0f",age);
-         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-           for(i=1, epj[j]=0.;i <=nlstate;i++) {
-             epj[j] += prlim[i][i]*eij[i][j][(int)age];
-             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+           fprintf(ficrest," %4.0f",age);
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+             }
+             epj[nlstate+1] +=epj[j];
            }
-           epj[nlstate+1] +=epj[j];
-         }
 
-         for(i=1, vepp=0.;i <=nlstate;i++)
-           for(j=1;j <=nlstate;j++)
-             vepp += vareij[i][j][(int)age];
-         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-         for(j=1;j <=nlstate;j++){
-           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(j=1;j <=nlstate;j++)
+               vepp += vareij[i][j][(int)age];
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           for(j=1;j <=nlstate;j++){
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+           }
+           fprintf(ficrest,"\n");
          }
-         fprintf(ficrest,"\n");
        }
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);